pipelines.patch

diff --git a/atac/callATACpeaks.sh b/atac/callATACpeaks.sh
index 4d3b537..8538a9c 100755
--- a/atac/callATACpeaks.sh
+++ b/atac/callATACpeaks.sh
@@ -37,12 +37,9 @@ fi
 
 peakFile="${readBed}.pf"
 
-# Shift reads by 75bp for peak calling
-adjustedBed="slopBed -i ${readBed} -g ${chrSize} -l 75 -r -75 -s"
-
 macs2 callpeak \
-    -t <(${adjustedBed}) -f BED -n "${peakFile}" -g "${genomeSize}" -p 1e-2 \
-    --nomodel --shift "${fragLen}" -B --SPMR --keep-dup all --call-summits
+    -t "${readBed}" -f BED -n "${peakFile}" -g "${genomeSize}" -p 1e-2 \
+    --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits
 
 if [[ ! -e "${peakFile}.fc.signal.bigwig" ]]
 then
@@ -52,6 +49,7 @@ then
     slopBed -i "${peakFile}_FE.bdg" -g "${chrSize}" -b 0 | \
         bedClip stdin "${chrSize}" "${peakFile}.fc.signal.bedgraph"
     rm -f "${peakFile}_FE.bdg"
+    bedSort "${peakFile}.fc.signal.bedgraph" "${peakFile}.fc.signal.bedgraph"
     bedGraphToBigWig "${peakFile}.fc.signal.bedgraph" "${chrSize}" "${peakFile}.fc.signal.bigwig"
     rm -f "${peakFile}.fc.signal.bedgraph"
 fi
@@ -66,6 +64,7 @@ then
     slopBed -i "${peakFile}_ppois.bdg" -g "${chrSize}" -b 0 | \
         bedClip stdin "${chrSize}" "${peakFile}.pval.signal.bedgraph"
     rm -f "${peakFile}_ppois.bdg"
+    bedSort "${peakFile}.pval.signal.bedgraph" "${peakFile}.pval.signal.bedgraph"
     bedGraphToBigWig "${peakFile}.pval.signal.bedgraph" "${chrSize}" "${peakFile}.pval.signal.bigwig"
     rm -f "${peakFile}.pval.signal.bedgraph"
 fi